I’m currently attempting to annotate and classify my gene sequence (CuMMO) using the lowest common ancestor algorithm and the results from BlastN through MEGAN.
I have prepared the necessary files for the alternative taxonomy (file of .tre and .map), and have successfully run it through the graphical interface on my macOS system.
However, I need to perform batch operations, so I tried running MEGAN on the Linux command line, during which I can’t seem to find the parameters for the alternative taxonomy in blast2lca. Do I need to use another plugin to replicate a similar process in MEGAN6? Thanks a lot for your attention and assistance !